Tumor associated antigens and methods of using the same

ABSTRACT

The present invention provides methods and compositions for the diagnosis of hyperproliferative disease and autoimmune disease. Tumor associated antigens, nucleic acids encoding them and antibodies to the tumor associated antigens are provided for the diagnosis of hyperproliferative disease, such as, for example, ovarian cancer, breast cancer, lung cancer, colorectal cancer, and other epithelial cancers, and for the diagnosis of autoimmune disease.

RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No. 10/106,559, filed Mar. 25, 2002, which claims the benefit of U.S. Provisional Patent Application Nos. 60/278,253, filed Mar. 23, 2001, and 60/278,237, filed Mar. 24, 2001, the disclosures of which are incorporated by reference herein.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This work was supported by U.S. Government grants numbers CA82724 and CA84359, awarded by the National Institutes of Health, and U.S. Department of Defense Grant Number OC970002. The U.S. Government may have certain rights in the invention.

BACKGROUND OF THE INVENTION

Ovarian carcinoma remains one of the most lethal gynecologic malignancies. It has been reported to be the fifth most common cancer and the fourth leading cause of cancer mortality among women in the United States (see Maller et al., SEER Cancer Statistics Review: 1973-1990, Bethesda, Md., National Cancer Institute(1993)).

Due to the lack of powerful diagnostic tests and also to the absence of any overt symptoms, early detection of ovarian cancer is difficult. In approximately two-thirds of patients, the disease is at an advanced stage (i.e., stage III or IV) at the time of diagnosis (see Boring et al., Ca. Cancer J. Clin. 44:7-26 (1994); Coppleson et al., Gynecologic Oncology: Fundamental Principles and Clinical Practice, 2nd ed, London, Churchill Livingstone Press (1992); Hung et al., “The Female Reproductive System: Cell Lines from Tumor of the Human Ovary and Uterus”, in Hay et al., Atlas of Human Tumor Cell Lines, Academic Press, San Diego, pp 359-386(1994)). Currently, diagnostic assays are limited to a few markers. Numerous studies on ovarian carcinomas have reported genetic alterations in oncogenes and tumor suppressor genes (see, e.g., Piver et al., Semin. Oncol. 18:177-85 (1991)). Specifically, amplification or activation of the oncogenes HER-2/neu, K-ras and c-myc, as well as inactivation of the tumor suppressor genes p53, BRCA1 and the human mismatch repair genes hMLH1, hMSH2, hPMS1 and hPMS2, have been detected in ovarian cancers. It has been reported that mutation of the p53 gene occurs in about 30-50% of ovarian cancers (see, e.g., Berchuck et al., Am. J. Obstet. Gynecol. 170:246-52 (1994)). p53 gene mutations are common in a variety of other tumors, however.

Accordingly, there exists a need to identify new markers associated with ovarian cancer and other epithelial cancers. The present invention satisfies this and other needs.

BRIEF SUMMARY OF THE INVENTION

The present invention provides methods and compositions for the diagnosis of hyperproliferative disease and autoimmune disease. Tumor associated antigens, nucleic acids encoding them and antibodies to the tumor associated antigens are provided for the diagnosis of hyperproliferative disease, such as, for example, ovarian cancer, breast cancer, lung cancer, colorectal cancer, and other epithelial cancers, and for the diagnosis of autoimmune disease.

In one aspect, methods for the prognosis or diagnosis of hyperproliferative disease are provided. The methods include obtaining a sample from the subject, the sample including antibodies, and contacting the sample with at least one tumor associated antigen. The tumor associated antigen can be ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. Complex formation is detected between the tumor associated antigen and the antibodies in the sample. Complex formation can indicate a prognosis or diagnosis of hyperproliferative disease. The subject can be a mammal, such as a human.

The sample can be blood, serum, ascites fluid, mucosal fluid, cervical wash, nipple aspirate fluid, stool, urine, saliva, tears, sputum, and the like. Complex formation can be detected by, for example, Western blot assay, radioimmunoassay, ELISA, sandwich immunoassay, immunoprecipitation assay, precipitin reaction, gel diffusion precipitin reaction, immunodiffusion assay, agglutination assay, complement-fixation assay, immunoradiometric assay, fluorescent immunoassay or protein A immunoassay. The hyperproliferative disease can be an epithelial cancer, such as ovarian cancer, breast cancer, lung cancer, colorectal cancer, and the like.

In another aspect, methods for prognosis or diagnosis of autoimmune disease in a subject are provided. The methods include obtaining a sample from the subject, the sample including antibodies. The sample is contacted with at least one tumor associated antigen. The tumor associated antigen can be, for example, ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAAO136, Osteonectin, F-box only protein 21, and/or ILF3. Complex formation between the tumor associated antigen and the antibodies in the sample is then detected. Complex formation can indicate a prognosis or diagnosis of autoimmune disease. The subject can be a mammal, such as a human.

The sample can be, for example, blood, serum, ascites fluid, mucosal fluid, cervical wash, nipple aspirate fluid, stool, urine or saliva. Complex formation can be detected by, for example, Western blot assay, radioimmunoassay, ELISA, sandwich immunoassay, immunoprecipitation assay, precipitin reaction, gel diffusion precipitin reaction, immunodiffusion assay, agglutination assay, complement-fixation assay, immunoradiometric assay, fluorescent immunoassay or protein A immunoassay.

The autoimmune disease can be, for example, rheumatoid arthritis, graft versus host disease, systemic lupus erythromatosis (SLE), scleroderma, multiple sclerosis, diabetes, organ rejection, inflammatory bowel disease, psoriasis, and the like.

In yet another aspect, methods for prognosis or diagnosis of hyperproliferative disease in a subject are provided. The methods include obtaining a sample from the subject and contacting the sample with at least one antibody to a tumor associated antigen. The tumor associated antigen can be, for example, ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. Complex formation between the antibody and tumor associated antigen in the sample is then detected. Complex formation can indicate a prognosis or diagnosis of hyperproliferative disease.

The subject can be a mammal, such as a human. The sample can be tissue, cells, plasma, serum, ascites fluid, mucosal fluid, cervical wash, nipple aspirate fluid, spinal fluid, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, hair, tumors, organs, stool, urine, tears, sputum, and the like. Complex formation can be detected by, for example, Western blot assay, radioimmunoassay, ELISA, sandwich immunoassay, immunoprecipitation assay, precipitin reaction, gel diffusion precipitin reaction, immunodiffusion assay, agglutination assay, complement-fixation assay, immunoradiometric assay, fluorescent immunoassay and/or protein A immunoassay. The hyperproliferative disease can be epithelial cancer, such as, for example, ovarian cancer, breast cancer, lung cancer, colorectal cancer, and the like.

In a related aspect, additional methods for prognosis or diagnosis of hyperproliferative disease in a subject are provided. The methods include contacting an array of probe molecules stably associated with a surface of a solid support with a sample of target nucleic acids under hybridization conditions sufficient to produce a hybridization pattern. The probe molecules can be nucleic acids encoding at least a fragment of at least one of ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. The hybridization pattern is detected to determine whether the subject has a hyperproliferative disease. The hybridization pattern can indicate a prognosis or diagnosis of hyperproliferative disease. The sample can be from, for example, ovary, lung, breast or the colorectal tract of the subject. The sample can also be tissue, cells, plasma, serum, ascites fluid, mucosal fluid, cervical wash, nipple aspirate fluid, spinal fluid, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, sputum, saliva, hair, tumors, organs, stool, or urine. The hyperproliferative disease can be epithelial cancer, such as, for example, ovarian cancer, lung cancer, breast cancer or colorectal cancer. The target nucleic acids can be labeled in one embodiment.

A kit for detecting antibodies to a tumor associated antigen is also provided. The kit includes at least one tumor associated antigen. The tumor associated antigen can be, for example, ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAAO136, Osteonectin, F-box only protein 21, and/or ILF3. The kit typically further includes anti-human antibody. In one embodiment, the tumor associated antigen is labeled; in another embodiment, the anti-human antibody is labeled.

A kit for detecting expression of tumor associated antigen genes is also provided. The kit can include nucleic acid primers to a tumor associated antigen nucleic acids. The tumor associated antigen nucleic acid can be, for example, ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. The kit typically further includes a polynucleotide polymerase, nucleotides, and/or a buffer. The kit can optionally further include an array of probe molecules for use in a hybridization assay.

DEFINITIONS

Prior to setting forth the invention in more detail, it may be helpful to a further understanding thereof to set forth definitions of certain terms as used hereinafter. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Only exemplary methods and materials are described, and any methods and materials similar to those described herein can be used in the practice or testing of the present invention. For purposes of the present invention, the following terms are defined below.

The terms “polynucleotide” and “nucleic acid” refer to a polymer composed of a multiplicity of nucleotide units (ribonucleotide or deoxyribonucleotide or related structural variants) linked via phosphodiester bonds. A polynucleotide or nucleic acid can be of substantially any length, typically from about six (6) nucleotides to about 10⁹ nucleotides or larger. Polynucleotides and nucleic acids include RNA, cDNA, genomic DNA, synthetic forms, and mixed polymers, both sense and antisense strands, and can also be chemically or biochemically modified or can contain non-natural or derivatized nucleotide bases, as will be readily appreciated by the skilled artisan. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, and the like), charged linkages (e.g., phosphorothioates, phosphorodithioates, and the like), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, and the like), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, and the like). Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in the art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of the molecule.

The term “oligonucleotide” refers to a polynucleotide of from about six (6) to about one hundred (100) nucleotides or more in length. Thus, oligonucleotides are a subset of polynucleotides. Oligonucleotides can be synthesized, for example, on an automated oligonucleotide synthesizer (for example, those manufactured by Applied BioSystems (Foster City, Calif.)), according to specifications provided by the manufacturer.

The term “primer” as used herein refers to a polynucleotide, typically an oligonucleotide, whether occurring naturally, as in an enzyme digest, or whether produced synthetically, which acts as a point of initiation of polynucleotide synthesis when used under conditions in which a primer extension product is synthesized. A primer can be single-stranded or double-stranded.

The term “polypeptide” refers to a polymer of amino acids and its equivalent and does not refer to a specific length of the product; thus, peptides, oligopeptides and proteins are included within the definition of a polypeptide. A “fragment” refers to a portion of a polypeptide having at least 6 contiguous amino acids, typically 8-10 contiguous amino acids, more typically at least 20 contiguous amino acids, still more typically at least 50 contiguous amino acids of the tumor associated antigen polypeptide. A derivative is a polypeptide having conservative amino acid substitutions, as compared with another sequence. Derivatives further include, for example, glycosylations, acetylations, phosphorylations, and the like. Further included within the definition of “polypeptide” are, for example, polypeptides containing one or more analogs of an amino acid (e.g., unnatural amino acids, and the like), polypeptides with substituted linkages as well as other modifications known in the art, both naturally and non-naturally occurring, as more fully described infra.

The terms “amino acid” or “amino acid residue”, as used herein, refer to naturally occurring L amino acids or to D amino acids. The commonly used one- and three-letter abbreviations for amino acids are used herein (see, e.g., Alberts et al., Molecular Biology of the Cell, Garland Publishing, Inc., New York (3d ed. 1994)).

The term “heterologous” refers to a nucleic acid or polypeptide from a different source, such as a tissue, organism or species, as compared with another nucleic acid or polypeptide.

The term “isolated” refers to a nucleic acid, polypeptide or antibody that has been removed from its natural cellular environment. An isolated nucleic acid is typically at least partially purified from other cellular nucleic acids, polypeptides and other constituents.

The terms “identical” or “percent identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms, or by visual inspection.

The phrase “substantially identical,” in the context of two nucleic acids or polypeptides, refers to two or more sequences or subsequences that have at least 60%, typically 80%, most typically 90-95% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms, or by visual inspection. An indication that two polypeptide sequences are “substantially identical” is that one polypeptide is immunologically reactive with antibodies raised against the second polypeptide.

“Similarity” or “percent similarity” in the context of two or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or conservative substitutions thereof, that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms, or by visual inspection. By way of example, a first amino acid sequence can be considered similar to a second amino acid sequence when the first amino acid sequence is at least 60%, 70%, 75%, 80%, 85%, 90%, or even 95% identical, or conservatively substituted, to the second amino acid sequence when compared to an equal number of amino acids as the number contained in the first sequence, or when compared to an alignment of polypeptides that has been aligned by a computer similarity program known in the art, as discussed below.

The term “substantial similarity” in the context of polypeptide sequences indicates that the polypeptide comprises a sequence with at least 70% sequence identity to a reference sequence, or typically 80%, or more typically 85% sequence identity or 90% sequence identity over a comparison window of about 10-20 amino acid residues. In the context of amino acid sequences, “substantial similarity” further includes conservative substitutions of amino acids. Thus, a polypeptide is substantially similar to a second polypeptide, for example, where the two peptides differ only by one or more conservative substitutions.

The term “conservative substitution,” when describing a polypeptide, refers to a change in the amino acid composition of the polypeptide that does not substantially alter the polypeptide's activity. Thus, a “conservative substitution” of a particular amino acid sequence refers to substitution of those amino acids that are not critical for polypeptide activity or substitution of amino acids with other amino acids having similar properties (e.g., acidic, basic, positively or negatively charged, polar or non-polar, etc.) such that the substitution of even critical amino acids does not substantially alter activity. Conservative substitution tables providing functionally similar amino acids are well known in the art. For example, the following six groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W). (See also Creighton, Proteins, W. H. Freeman and Company (1984).) In addition, individual substitutions, deletions or additions that alter, add or delete a single amino acid or a small percentage of amino acids in an encoded sequence are also “conservative substitutions.”

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

Optimal alignment of sequences for comparison can be conducted, for example, by the local homology algorithm of Smith and Waterman (Adv. Appl. Math. 2:482 (1981)), by the homology alignment algorithm of Needleman and Wunsch (J. Mol. Biol. 48:443 (1970)), by the search for identity method of Pearson and Lipman (Proc. Natl. Acad. Sci. USA 85:2444 (1988)), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally Ausubel et al., Current Protocols in Molecular Biology, 4th ed., John Wiley and Sons, New York (1999)).

One example of a useful algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments to show relationship and percent sequence identity. It also plots a tree or dendogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng and Doolittle (J. Mol. Evol. 35:351-60 (1987)). The method used is similar to the CLUSTAL method described by Higgins and Sharp (Gene 73:237-44 (1988); CABIOS 5:151-53 (1989)). The program can align up to 300 sequences, each of a maximum length of 5,000 nucleotides or amino acids. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster is then aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences are aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison and by designating the program parameters. For example, a reference sequence can be compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps.

Another example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al. (J. Mol. Biol. 215:403-10 (1990)). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always<0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul, Proc. Natl. Acad. Sci. USA 90:5873-87 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is typically less than about 0.1, more typically less than about 0.01, and most typically less than about 0.001. Another indication that two nucleic acids are substantially identical is that the two molecules hybridize specifically to each other under stringent conditions.

The phrase “hybridizing specifically to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. “Bind(s) substantially” refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence.

“Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments, such as Southern and northern hybridization, are sequence-dependent, and are different under different environmental parameters. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes (part I, chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” Elsevier, N.Y. (1993), which is incorporated by reference herein). Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. Typically, under “stringent conditions,” a probe will hybridize to its target subsequence, but not to other sequences.

The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the T_(m) for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formamide in 4-6×SSC or SSPE at 42° C., or 65-68° C. in aqueous solution containing 4-6×SSC or SSPE. An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes. (See generally Sambrook et al., Molecular Cloning, A Laboratory Manual, 3rd ed., Cold Spring Harbor Publish., Cold Spring Harbor, N.Y. (2001), which is incorporated by reference herein.) Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example of medium stringency wash for a duplex of, for example, more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example of a low stringency wash for a duplex of, for example, more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30° C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.

The term “immunologically cross-reactive” means that a polypeptide, fragment, derivative or analog is capable of competitively inhibiting the binding of an antibody to its antigen.

The term “sample” generally indicates a specimen of tissue, cells, plasma, serum, ascites fluid, mucosal fluid, cervical wash, nipple aspirate fluid, spinal fluid, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, hair, tumors, organs, stool, urine, other material of biological origin that contains antibodies, polypeptide and/or polynucleotides, or in vitro cell culture constituents of any of these. A sample can further be semi-purified or purified forms of antibodies, polypeptides and/or polynucleotides. A sample can be isolated from a mammal, such as a human, an animal, any other organism as well as in vitro culture constituents of any of these.

The term “proliferation” refers to activities such as growth, reproduction, change in gene expression, transformation, and other changes in cell state. “Hyper-proliferation” refers to an increase in one or more proliferative activities, as compared with normal cells or tissue. “Hyperproliferative disease” refers to a disease, condition, or disorder associated with hyperproliferation of cells or tissues in a subject. Diseases involving hyper-proliferation include, but are not limited to, cancer, malignancies, premalignant conditions (e.g., hyperplasia, metaplasia, dysplasia), benign tumors, hyperproliferative disorders, benign dysproliferative disorders, autoimmune diseases, and the like.

The term “antibody” refers to a polypeptide substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, that specifically binds and recognizes an analyte (antigen). Immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.

An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain has a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms “variable light chain” (or “V_(L)”) and “variable heavy chain” (or “V_(H)”) refer to these light and heavy chains, respectively.

Antibodies exist, for example, as intact immunoglobulins or as a number of well characterized antigen-binding fragments produced by digestion with various peptidases. For example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce an F(ab′)₂ fragment, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab′)₂ fragment can be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab′)₂ dimer into an Fab′ monomer. The Fab′ monomer is essentially an Fab with part of the hinge region (see Fundamental Immunology, Third Edition, W. E. Paul (ed.), Raven Press, N.Y. (1993)). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments can be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments, such as a single chain antibody, an antigen binding F(ab′)₂ fragment, an antigen binding Fab′ fragment, an antigen binding Fab fragment, an antigen binding Fv fragment, a single heavy chain or a chimeric antibody. Such antibodies can be produced by the modification of whole antibodies or synthesized de novo using recombinant DNA methodologies. (See, e.g., Harlow and Lane, Using Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1999), the disclosure of which is incorporated by reference herein.)

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

The present invention provides methods and compositions for the diagnosis of hyperproliferative disease and/or autoimmune disease. Tumor associated antigens, nucleic acids encoding them and antibodies to the tumor associated antigens are provided for the diagnosis of hyperproliferative disease, such as, for example, ovarian cancer, breast cancer, lung cancer, colorectal cancer, and other epithelial cancers, and/or for the diagnosis of autoimmune disease.

Tumor Associated Antigen Nucleic Acids

In one aspect, nucleic acids encoding tumor associated antigen are provided as markers of hyperproliferative disease or autoimmune disease. Such tumor associated antigen nucleic acids can include, for example, proteins, fragments, derivatives and analogs thereof, the function (e.g., expression or activity) of which is altered in cells associated with hyperproliferative disease and/or autoimmune disease. The tumor associated antigen nucleic acids can also encode polypeptides of normal function, but which are differentially immunogenic in the context of cells associated with hyperproliferative disease and/or autoimmune disease as compared with normal epithelial cells of the same tissue or cell type.

The tumor associated antigen nucleic acids can include, for example, nucleic acids encoding a zinc finger-containing protein ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. The tumor associated antigen nucleic acids can further include those encoding the tumor suppressor gene p53 and/or the cancer-testis antigen NY-ESO-1. Such tumor associated antigen nucleic acids can include nucleic acids from human and non-human mammals, such as, for example, porcine, bovine, feline, equine, and/or canine species, as well as primate species.

In some embodiments, the tumor associated antigen nucleic acids correspond to human nucleic acid sequences encoding ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. The tumor associated antigen nucleic acids can further include those encoding the tumor suppressor gene p53 and/or the cancer-testis antigen NY-ESO-1. In specific embodiments, the tumor associated antigen nucleic acids correspond to the following nucleic acids, which are referenced by their National Center for Biotechnology Information Unigene accession numbers: ZFP161 (Hs.156000; ZFP161); Ubiquilin-1 (Hs.9589; UBQLN1); HOX-B6 (Hs.98428; HOXB6); IFI27 (Hs.278613; IFI27); YB-1 (Hs.74497; NSEP1); KIAA0136 (Hs.70359; KIAA0316); Osteonectin (Hs.111779; SPARC); F-box only protein 21 (Hs.184227; FBXO21); ILF3 (Hs.256583; ILF3), or the coding regions thereof. The tumor associated antigen nucleic acids can additionally correspond to the nucleic acids encoding p53 (Hs.1846; TP53); NY-ESO-1 (Hs. 167379; CTAG1), or the coding regions thereof. (All of these sequences are incorporated by reference herein in their entirety.)

The invention also provides fragments of tumor associated antigen nucleic acids comprising at least 6 contiguous nucleotides (i.e., a hybridizable portion); in other embodiments, the nucleic acids comprise contiguous nucleotides of at least 10 nucleotides, 15 nucleotides, 25 nucleotides, 50 nucleotides, 100 nucleotides, 150 nucleotides, 200 nucleotides, or 250 nucleotides of a tumor associated antigen nucleic acid sequence. The nucleic acids can also be smaller than 35, 200 or 250 nucleotides in length. Nucleic acids can be single or double stranded. As used herein, a “nucleic acid encoding a fragment or portion of a tumor associated antigen polypeptide” refers to a nucleic acid encoding only the recited fragment or portion of the tumor associated antigen polypeptide and not the other contiguous portions of the tumor associated antigen polypeptide as a continuous sequence. Fragments of tumor associated antigen nucleic acids comprising regions conserved between other tumor associated antigen nucleic acids, of the same or different species, are also provided. Nucleic acids encoding one or more tumor associated antigen domains are also provided.

The invention also relates to nucleic acids hybridizable to or complementary to the foregoing sequences. In specific aspects, nucleic acids are provided which comprise a sequence complementary to at least 10, 15, 25, 50, 100, 200, or 250 nucleotides of a tumor associated antigen gene, or a portion thereof. In a specific embodiment, a nucleic acid which is hybridizable to a tumor associated antigen nucleic acid, or to a nucleic acid encoding a tumor associated antigen derivative, under conditions of low, medium or high stringency is provided. Low, moderate and high stringency conditions are well known to those of skill in the art, and will vary predictably depending on the base composition of the particular nucleic acid sequence and on the specific organism from which the nucleic acid sequence is derived. For guidance regarding such conditions see, for example, Sambrook et al. (supra); and Ausubel et al. (supra) (both of which are incorporated by reference herein).

Nucleic acids encoding derivatives and analogs of tumor associated antigen proteins, and tumor associated antigen antisense nucleic acids are additionally provided. Derivatives of the tumor associated antigen sequences include those nucleotide sequences encoding substantially the same amino acid sequences as found in native tumor associated antigen proteins, and those encoded amino acid sequences with functionally equivalent amino acids (e.g., conservative substitutions).

Tumor associated antigen nucleic acids can be obtained by standard procedures known in the art (e.g., by chemical synthesis, by cDNA cloning, by the cloning of genomic DNA, by PCR amplification, and the like. (See, e.g., Sambrook et al., supra; Glover (ed.), DNA Cloning: A Practical Approach, MRL Press, Ltd., Oxford, U.K. Vol. I, II (1995); Ausubel et al., supra; the disclosures of which are incorporated by reference herein.) The nucleic acids can also identified by searching nucleic databases for nucleic acid sequences that are substantially similar to known tumor associated antigen nucleic acid sequences.

Tumor Associated Antigen Polypeptides

In another aspect, the invention relates to tumor associated antigen polypeptide markers of hyperproliferative disease, such as epithelial cancers. The invention further relates to tumor associated antigen polypeptide markers of autoimmune disease. Such tumor associated antigen polypeptides can include, for example, proteins, fragments, derivatives and analogs thereof, the function (e.g., expression or activity) of which is altered in cells associated with hyperproliferative disease and/or autoimmune disease. The tumor associated antigens also include polypeptides of normal function, but which are differentially immunogenic in cells associated with hyperproliferative disease and/or autoimmune disease as compared with normal epithelial cells of the same tissue or cell type.

Tumor associated antigen polypeptides include, for example, Ubiquilin-1, IFI27, HOX-B6, ZFP161, YB-1, KIAA0136, Osteonectin, F-box only protein 21, or ILF3, alone or in combination with p53, NY-ESO-1, and/or fragments, derivatives or analogs of any of these, as further discussed below. The tumor associated antigens include polypeptides from human and non-human mammals, such as, for example, porcine, bovine, feline, equine, and/or canine species, as well as other primate species.

In some embodiments, the tumor associated antigen polypeptides are human Ubiquilin-1, IFI27, HOX-B6, ZFP161, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3, alone or in combination with p53, NY-ESO-1, and/or fragments, derivatives or analogs thereof. In specific embodiments, the tumor associated antigens have the deduced amino acid sequences of the following tumor associated antigen nucleic acid sequences (which are referenced by their National Center for Biotechnology Information Unigene accession numbers): Ubiquilin-1 (Hs.9589; UBQLN1); IFI27 (Hs.278613; IFI27); HOX-B6 (Hs.98428; HOXB6); ZFP161 (Hs.156000; ZFP161); YB-1 (Hs.74497; NSEP1); KIAA0136 (Hs.70359; KIAA0316); Osteonectin (Hs. 111779; SPARC); F-box only protein 21 (Hs.184227; FBXO21); and/or ILF3 (Hs.256583; ILF3). The tumor associated antigens can also have the deduced amino acid sequences of p53 (Hs.1846; TP53) and/or NY-ESO-1 (Hs. 167379; CTAG1), or fragments thereof.

Tumor associated antigen polypeptide derivatives include naturally-occurring amino acid sequence variants as well as those altered by substitution, addition or deletion of one or more amino acid residues. Tumor associated antigen polypeptide derivatives include, but are not limited to, those containing as a primary amino acid sequence all or part of the amino acid sequence of a tumor associated antigen polypeptide, including altered sequences in which one or more functionally equivalent amino acid residues (e.g., a conservative substitution) are substituted for residues within the sequence, resulting in a silent change.

In another aspect, a polypeptide consisting of or comprising a fragment of a tumor associated antigen polypeptide having at least 10 contiguous amino acids of the tumor associated antigen polypeptide is provided. In other embodiments, the fragment has at least 20 or 50 contiguous amino acids of the tumor associated antigen polypeptide. The fragments can also be smaller than 35, 100 or 200 amino acids.

Fragments, derivatives or analogs of tumor associated antigen polypeptides include, but are not limited to, those molecules comprising regions that are substantially similar to tumor associated antigen polypeptide or fragments thereof (e.g., in various embodiments, at least 70%, 75%, 80%, 90%, or even 95% identity or similarity over an amino acid sequence of identical size), or when compared to an aligned sequence in which the alignment is done by a computer sequence comparison/alignment program known in the art, or whose coding nucleic acid is capable of hybridizing to a tumor associated antigen nucleic acid, under high stringency, moderate stringency, or low stringency conditions (supra).

Tumor associated antigen polypeptide fragments, derivatives and analogs can be produced by various methods known in the art. The manipulations which result in their production can occur at the gene or protein level. For example, the cloned tumor associated antigen nucleic acids can be modified by any of numerous strategies known in the art (see, e.g., Sambrook et al., supra), such as making conservative substitutions, deletions, insertions, and the like. The sequence can be cleaved at appropriate sites with restriction endonuclease(s), followed by further enzymatic modification if desired, isolated, and ligated in vitro. In the production of the tumor associated antigen nucleic acids encoding a fragment, derivative or analog of a tumor associated antigen polypeptide, the modified nucleic acid typically remains in the proper translational reading frame, so that the reading frame is not interrupted by translational stop signals or other signals which interfere with the synthesis of the tumor associated antigen fragment, derivative or analog. Tumor associated antigen nucleic acids can also be mutated in vitro or in vivo to create and/or destroy translation, initiation and/or termination sequences. The tumor associated antigen-encoding nucleic acid can also be mutated to create variations in coding regions and/or to form new restriction endonuclease sites or destroy preexisting ones and to facilitate further in vitro modification. Any technique for mutagenesis known in the art can be used, including but not limited to, chemical mutagenesis, in vitro site-directed mutagenesis (Hutchison et al., J. Biol. Chem. 253:6551-60 (1978); Sambrook et al., supra), and the like.

Manipulations of the tumor associated antigen polypeptide sequence can also be made at the polypeptide level. Included within the scope of the invention are tumor associated antigen polypeptide fragments, derivatives or analogs which are differentially modified during or after synthesis (e.g., in vivo or in vitro translation). Such modifications include conservative substitution, glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand, and the like. Any of numerous chemical modifications can be carried out by known techniques, including, but not limited to, specific chemical cleavage (e.g., by cyanogen bromide), enzymatic cleavage (e.g., by trypsin, chymotrypsin, papain, V8 protease, and the like); modification by, for example, NaBH₄ acetylation, formylation, oxidation and reduction, metabolic synthesis in the presence of tunicamycin, and the like.

In addition, tumor associated antigen polypeptides, fragments, derivatives and analogs can be chemically synthesized. For example, a peptide corresponding to a portion, or fragment, of a tumor associated antigen polypeptide, which comprises a desired domain, or which mediates a desired activity in vitro, can be synthesized by use of chemical synthetic methods using, for example, an automated peptide synthesizer. Furthermore, if desired, nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the tumor associated antigen polypeptide sequence. Non-classical amino acids include but are not limited to the D-isomers of the common amino acids, α-amino isobutyric acid, 4-aminobutyric acid, 2-amino butyric acid, γ-amino butyric acid, 6-amino hexanoic acid, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, selenocysteine, fluoro-amino acids, designer amino acids such as β-methylamino acids, C α-methyl amino acids, N α-methylamino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary).

In a specific embodiment, the tumor associated antigen polypeptide, fragment, derivative or analog is a chimeric, or fusion, protein comprising a tumor associated antigen polypeptide, fragment, derivative or antigen thereof (typically containing at least a domain or motif of the tumor associated antigen polypeptide, or at least 10 contiguous amino acids of the tumor associated antigen polypeptide) joined at its amino- or carboxy-terminus via a peptide bond to an amino acid sequence of a different protein. In one embodiment, such a chimeric protein is produced by recombinant expression of a nucleic acid encoding the protein. The chimeric product can be made by ligating the appropriate nucleic acid sequences, encoding the desired amino acid sequences, to each other in the proper coding frame and expressing the chimeric product by methods commonly known in the art. Alternatively, the chimeric product can be made by protein synthetic techniques (e.g., by use of an automated peptide synthesizer).

The production and use of tumor associated antigen polypeptides, fragments, derivatives and analogs thereof are also within the scope of the present invention. In a specific embodiment, the polypeptide, fragment, derivative or analog is immunogenic or antigenic (e.g., that can be recognized by an antibody specific for the tumor associated antigen polypeptide) by immune cell such as T cells. As one example, such fragments, derivatives or analogs which have the desired immunogenicity or antigenicity can be used, for example, in immunoassays, for immunization, and the like. A specific embodiment relates to a tumor associated antigen fragment that can be bound by an anti-tumor associated antigen antibody, such as an antibody in a sample from a subject. Fragments, derivatives or analogs of tumor associated antigen can be tested for the desired activity by methods known in the art.

Tumor associated antigen polypeptides can be isolated and purified by standard methods including chromatography (e.g., ion exchange, affinity, sizing column chromatography, high pressure liquid chromatography, and like), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. The functional properties can be evaluated using any suitable assay as described herein or otherwise known to the skilled artisan. Alternatively, once a tumor associated antigen polypeptide produced by a recombinant host cell is identified, the amino acid sequence of the polypeptide can be deduced from the nucleotide sequence of the chimeric gene contained in the recombinant host cell. As a result, the protein can be synthesized by standard chemical methods known in the art (see, e.g., Hunkapiller et al., Nature 310:105-11 (1984); Stewart and Young, Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Co., Rockford, Ill., (1984)).

In another alternate embodiment, native tumor associated antigen polypeptides can be purified from natural sources by standard methods such as those described above (e.g., immunoaffinity purification). In a specific embodiment of the present invention, tumor associated antigen polypeptides, whether produced by recombinant DNA techniques, by chemical synthetic methods or by purification of native polypeptides include, but are not limited to, those containing as a primary amino acid sequence all or part of the amino acid sequence of tumor associated antigen polypeptide, as well as fragments, derivatives and analogs thereof.

Antibodies to Tumor Associated Antigens

Antibodies against tumor associated antigens are also provided. The antibodies are typically immunospecific for tumor associated antigens, such as, for example, Ubiquilin-1, IFI27, HOX-B6, ZFP161, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3, or fragments, derivative or analogs thereof. The antibodies can further include those against p53 or NY-ESO-1, or fragments, derivative or analogs thereof. In specific embodiments, the antibodies are immunospecific for human tumor associated antigens.

Tumor associated antigen antibodies include, but are not limited to, polyclonal antibodies, monoclonal antibodies, chimeric antibodies, single chain antibodies, antigen binding antibody fragments (e.g., Fab, Fab′, F(ab′)₂, Fv, or hypervariable regions), bi-specific antibodies, and an Fab expression library. In some embodiments, polyclonal and/or monoclonal antibodies to a tumor associated antigen are produced. In other embodiments, antibodies to a domain of a tumor associated antigen are produced. In yet other embodiments, fragments of a tumor associated antigen that are identified as immunogenic are used as immunogens for antibody production.

Various procedures known in the art can be used for the production of polyclonal antibodies. For the production of such antibodies, various host animals (including, but not limited to, rabbits, mice, rats, sheep, goats, camels, and the like) can be immunized by injection with a tumor associated antigen, fragment, derivative or analog. Various adjuvants can be used to increase the immunological response, depending on the host species. Such adjuvants include, for example, Freund's adjuvant (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and other adjuvants, such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum.

For preparation of monoclonal antibodies directed toward a tumor associated antigen, any technique that provides for the production of antibody molecules by continuous cell lines in culture can be used. Such techniques include, for example, the hybridoma technique originally developed by Kohler and Milstein (see, e.g., Nature 256:495-97 (1975)), the trioma technique (see, e.g., Hagiwara and Yuasa, Hum. Antibodies Hybridomas 4:15-19 (1993); Hering et al., Biomed. Biochim. Acta 47:211-16 (1988)), the human B-cell hybridoma technique (see, e.g., Kozbor et al., Immunology Today 4:72 (1983)), and the EBV-hybridoma technique to produce human monoclonal antibodies (see, e.g., Cole et al., In: Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96 (1985)). Human antibodies can be used and can be obtained by using human hybridomas (see, e.g., Cote et al., Proc. Natl. Acad. Sci. USA 80:2026-30 (1983)) or by transforming human B cells with EBV virus in vitro (see, e.g., Cole et al., supra).

Further to the invention, “chimeric” antibodies (see, e.g., Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-55 (1984); Neuberger et al., Nature 312:604-08 (1984); Takeda et al., Nature 314:452-54 (1985)) can be prepared. Such chimeric antibodies are typically prepared by splicing the genes (of one species) for an antibody molecule specific for tumor associated antigen together with genes from another species of antibody molecule of appropriate biological activity. It can be desirable to transfer the antigen binding regions (e.g., Fab′, F(ab′)₂, Fab, Fv, or hypervariable regions) of antibodies from one species into the framework of an antibody from another species by recombinant DNA techniques to produce a chimeric molecule. Methods for producing such “chimeric” molecules are generally well known and described in, for example, U.S. Pat. Nos. 4,816,567; 4,816,397; 5,693,762; and 5,712,120; PCT Patent Publications WO 87/02671 and WO 90/00616; and European Patent Publication EP 239 400 (the disclosures of which are incorporated by reference herein). In a specific embodiment, a human monoclonal antibody or portion(s) thereof can be identified by screening a human B-cell cDNA library for nucleic acid molecules that encode antibodies that specifically bind to a tumor associated antigen according to the method generally set forth by Huse et al. (Science 246:1275-81 (1989)). The nucleic acid molecule can then be cloned and amplified to obtain sequences that encode the antibody (or antigen-binding domain) of the desired specificity. Phage display technology offers another technique for selecting antibodies that bind to tumor associated antigens, fragments, derivatives or analogs thereof. (See, e.g., International Patent Publications WO 91/17271 and WO 92/01047; Huse et al., supra.)

According to another aspect of the invention, techniques described for the production of single chain antibodies (see, e.g., U.S. Pat. Nos. 4,946,778 and 5,969,108) can be used. An additional aspect of the invention utilizes the techniques described for the construction of a Fab expression library (see, e.g., Huse et al., supra) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for tumor associated antigens, fragments, derivatives, or analogs thereof.

Antibody fragments that contain the idiotype of the molecule can be generated by known techniques. For example, such fragments include but are not limited to, the F(ab′)₂ fragment which can be produced by pepsin digestion of the antibody molecule, the Fab′ fragments which can be generated by reducing the disulfide bridges of the F(ab′)₂ fragment, the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent, and Fv fragments. Recombinant Fv fragments can also be produced in eukaryotic cells using, for example, the methods described in U.S. Pat. No. 5,965,405 (the disclosure of which is incorporated by reference herein).

In another embodiment, bi-specific antibodies are provided. Bi-specific antibodies can be monoclonal antibodies that have binding specificities for at least two different antigens. For example, one of the binding specificities can be for a tumor associated antigen and the other one is for any other antigen. Alternatively, one specificity is for a first tumor associated antigen, while the other specificity is for a second, different tumor associated antigen.

Methods for making bi-specific antibodies are known in the art. Traditionally, the recombinant production of bi-specific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (see, e.g., Milstein and Cuello, Nature 305:537-39 (1983), the disclosure of which is incorporated by reference herein). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of different antibody molecules, some of which have the desired bi-specific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in PCT Patent Publication WO 93/08829, and in Traunecker et al (EMBO J. 10:3655-59 (1991)) (the disclosures of which are incorporated by reference herein).

Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion typically is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. The first heavy-chain constant region (CH1) containing the site necessary for light-chain binding is usually present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bi-specific antibodies see, for example, Suresh et al. (Methods in Enzymology 121:210 (1986), the disclosure of which is incorporated by reference herein).

In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art (e.g., ELISA (enzyme-linked immunosorbent assay)). (See, e.g., Harlow and Lane, supra.)

Diagnostics

Methods and compositions for diagnosis of hyperproliferative disease or autoimmune disease are also provided. Such methods and compositions can be used to detect, prognose, diagnose, or monitor hyperproliferative disease or autoimmune disease associated with aberrant changes in tumor associated antigen expression, activity and/or immunogenicity.

In a typical embodiment, a sample can be obtained from a subject. The sample can be contacted with at least one tumor associated antigen, or antibody to at least one tumor associated antigen. The tumor associated antigen is typically ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAAO136, Osteonectin, F-box only protein 21, and/or ILF3. Complex formation of the tumor associated antigen or antibody with antibody or tumor associated antigen in the sample can be detected. In certain embodiments, complex formation from the sample can be compared with complex formation from a control sample (e.g., normal tissue or cells, tissue or cells not having aberrant changes in tumor associated antigen expression, activity and/or immunogenicity, serum from a healthy subject, and the like).

A prognosis or diagnosis of the presence of hyperproliferative disease or autoimmune disease in the subject can be indicated by the presence of antigen:antibody complexes. Such a positive diagnosis can optionally indicate a need for further testing, such as, for example, sonograph, ultrasound, biopsy, exploratory surgery, and the like. Thus, in some embodiments, the methods and composition can comprise a screen or prescreen for detection of hyperproliferative and/or autoimmune disease.

Tumor associated antigen polypeptides (including fragments, derivatives, and analogs thereof), tumor associated antigen nucleic acids (and sequences complementary thereto), and anti-tumor associated antigen antibodies have uses in diagnostics to detect, prognose, diagnose, or monitor hyperproliferative disease or autoimmune disease. Such hyperproliferative diseases include, but are not limited to, epithelial cancers, such as ovarian cancer, breast cancer, lung cancer, colorectal cancer, and the like. As will be appreciated by the skilled artisan, although the following discussion exemplifies method and compositions for use in the diagnosis, detection, prognosis, or monitoring of hyperproliferative disease, such assays can also be used to diagnose, detect, prognose, or monitor autoimmune disease. The autoimmune disease can be, for example, rheumatoid arthritis, graft versus host disease, systemic lupus erythromatosis (SLE), sclerodemma, multiple sclerosis, diabetes, organ rejection, inflammatory bowel disease, psoriasis, and the like.

In one aspect, immunoassays are used to detect antibodies in a subject (“autoimmune antibodies”) against one or more of the tumor associated antigens. For example, immunoassays can be used to detect autoimmune antibodies against Ubiquilin-1, IFI27, HOX-B6, ZFP161, YB-1, KIAAO136, Osteonectin, F-box only protein 21, and/or ILF3 in a sample from a subject. The immunoassays can also be used to detect p53, and/or NY-ESO-1. The presence of antibody to one or more of these tumor associated antigen is an indication of a hyperproliferative disease in the subject.

Immunoassays which can be used to detect such autoimmune antibodies include, for example, competitive and non-competitive assay systems such as Western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, and the like. (See, e.g., Harlow and Lane, Using Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1999).)

Immunoassays can be carried out, for example, by contacting a subject sample with tumor associated antigen polypeptide under conditions such that immunospecific binding (complex formation) can occur, and detecting or measuring the amount of any immunospecific binding of antibody to the tumor associated antigen. The tumor associated antigen can be used to detect the presence (e.g., high, low or absence) of antibody against tumor associated antigens in blood, serum, ascites fluid, mucosal fluid (e.g., cervical fluids), and the like, in a sample from a subject.

For example, autoimmune antibodies in a subject sample can be detected by the following method. The tumor associated antigen (or a fragment, derivative and/or analog thereof) is immobilized on a matrix. Then, a sample to be assayed (e.g., blood, serum, ascites fluid, mucosal fluid, and the like) is added and allowed to react at a temperature suitable for immunospecific binding (e.g., from about 4° C. to about 40° C.).

Following the binding reaction, the matrix is washed and then a secondary antibody is added to the reaction mixture; the secondary antibody typically immunospecifically binds to the subject antibodies (e.g., anti-human antibodies). The secondary antibody is allowed to react with autoimmune antibodies bound to the tumor associated antigen on the matrix.

The secondary antibody can be detectably labeled with, for example, a fluorescent substance, a chromogenic substance, a chemiluminescent substance, an enzyme, a radioisotope, by biotinyl moieties, and the like. Examples of detectable labels include, but are not limited to, the following: radioisotopes (e.g., ³H, ¹⁴C, ³²P, ³⁵S, ¹²⁵I, ¹³¹I, and the like), fluorescent molecules (e.g., fluorescein isothiocyanate (FITC), rhodamine, phycoerythrin (PE), phycocyanin, allophycocyanin, ortho-phthaldehyde, fluorescamine, peridinin-chlorophyll a (PerCP), Cy3 (indocarbocyanine), Cy5 (indodicarbocyanine), lanthanide phosphors, and the like), enzymes (e.g., horseradish peroxidase, β-galactosidase, luciferase, alkaline phosphatase), biotinyl groups, and the like. In some embodiments, detectable labels are attached by spacer arms of various lengths to reduce potential steric hindrance.

The reaction mixture is then washed to remove unbound secondary antibody, and the secondary antibody bound to the matrix is detected. For example, bound, labeled secondary antibody can be detected by standard colorimetric, radioactive, photometric and/or fluorescent detection means. Detection reagents can be used, if needed. For fluorescent labels, signal can be detected by, for example, a scanning confocal microscope in photon counting mode. Appropriate scanning devices are described by, for example, U.S. Pat. Nos. 5,578,832 and 5,631,734 (both incorporated by reference herein). For antibodies labeled with biotin, the reaction can be treated with the appropriate streptavidin-conjugate (e.g., streptavidin-horseradish peroxidase, streptavidin-alkaline phosphatase, streptavidin-luciferase, and the like) and then treated with the appropriate reagents for colorimetric or photometric detection. For radiolabeled antibody, signal can be detected using a scintillation counter, phosphoimager or similar device. Alternatively, the secondary antibody can be unlabeled, and the presence of autoimmune antibodies against a tumor associated antigen is detected using a labeled tertiary antibody.

Any suitable matrix can be used for immobilizing the tumor associated antigen. For example, for ELISA, the tumor associated antigen can be immobilized on ELISA plates, microtiter plates, and the like. In one embodiment, histidine-tagged tumor associated antigen is bound to H isSorb ELISA plates (Quiagen). Alternatively, the tumor associated antigen can be immobilized in a sandwich assay.

Autoimmune antibody can also be detected in a conventional Western blotting assay, such as by immobilizing at least one tumor associated antigen to a solid support matrix, such as, for example, nitrocellulose membrane, nylon membrane, PVDF membrane, and the like.

The tumor associated antigens can also be immobilized on other matrices. The matrices can have virtually any possible structural configuration so long as the immobilized antigen is capable of binding to an antibody. Thus, the support configuration can be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface can be flat such as a sheet, test strip, and the like.

Suitable matrices include, for example, gel beads (e.g., Sepharose 4B, Sepharose 6B (Pharmacia Fine Chemicals (Sweden))), dextran gel (e.g., Sephadex G-75, Sephadex G-100, Sephadex G-200 (Pharmacia Fine Chemicals (Sweden))), polyacrylamide gel (e.g., Bio-Gel P-30, Bio-Gel P-60, Bio-Gel P-100 (Bio-Rad Laboratories USA)), cellulose beads (e.g., Avicel (Asahi Chemical Industry Co. Ltd.)), ion exchange cellulose (e.g., diethylaminoethylcellulose, carboxymethylcellulose), physical adsorbents (e.g., glass (glass beads, glass rods, aminoalkyl glass beads, aminoalkyl glass rods)), silicone flakes, styrenic resin (e.g., polystyrene beads, polystyrene particles), immunoassay plates (e.g., Nunc (Denmark)), ion exchange resin (e.g., weakly acidic cation exchange resin (e.g., Amberlite IRC-5 (Rohm & Haas Company (U.S.A.)), Zeo-Karb 226 (Permutit (West Germany)), and weakly basic anion exchange resin (e.g., Amberlite IR-4B, Dowex 3 (Dow Chemical (U.S.A.)))), and the like.

Immunoassays to detect autoimmune antibody in a subject sample can also be performed, for example, by contacting a subject sample with a labeled tumor associated antigen polypeptide under conditions such that immunospecific binding can occur (complex formation), and detecting or measuring the amount of immunospecific complex formation. Such immunoassays can include, for example, immunoprecipitations and RIA's.

Tumor associated antigen can be labeled with, for example, a fluorescent substance, a chromogenic substance, a chemiluminescent substance, an enzyme, a radioisotope, by biotinyl moieties, and the like, as described supra.

Diagnostic assays can also be performed to qualitatively or quantitatively detect tumor associated antigen in a subject sample. For example, immunoassays can be used to detect one or more of the following tumor associated antigens in a subject sample: Ubiquilin-1, IFI27, HOX-B6, ZFP161, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. The immunoassays can also be used to detect p53, and/or NY-ESO-1 in a sample from a subject.

For example, immunoassays to detect tumor associated antigen can be carried out by a method comprising contacting a sample derived from a subject with an anti-tumor associated antigen antibody under conditions such that immunospecific binding (complex formation) can occur, and detecting or measuring the amount of any immunospecific binding. In a specific aspect, binding of antibody to tissue sections from a subject can be used to detect aberrant (e.g., high, low or absent) levels of tumor associated antigen and/or aberrant tumor associated antigen localization. By “aberrant levels,” is meant increased or decreased levels or immunogenicity relative to that present, or a standard level representing that present, in an analogous sample from a samples, a portion of the body or from a subject not having the hyperproliferative disease.

In a specific embodiment, antibody to tumor associated antigen can be used to assay a subject's tissue, serum or other biological sample for the presence of tumor associated antigen, where an aberrant level or immunogenicity of the tumor associated antigen is an indication of a hyperproliferative disease (e.g., an epithelial cancer). The immunoassays which can be used to detect tumor associated antigen include, for example, competitive and non-competitive assay systems using techniques such as Western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, and the like. (See, e.g., Harlow and Lane, Using Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1999).)

For example, antibodies can be used to quantitatively or qualitatively detect the presence of tumor associated antigens using immunofluorescence techniques employing a fluorescently labeled antibody (see, e.g., supra) coupled with light microscopic, flow cytometric, or fluorimetric detection. Such techniques can be used for the detection of tumor associated antigens that are expressed on the cell surface. Thus, the techniques described herein can be used to detect specific cells, within a population of cells, having altered tumor associated antigen expression or immunogenicity.

Immunoassays can also be employed histologically, as in immunofluorescence or immunoelectron microscopy, for in situ detection of tumor associated antigen. In situ detection can be accomplished by removing a histological sample from a subject, and contacting the sample with a labeled antibody. The antibody is typically contacted with the sample by overlaying the labeled antibody onto the sample. Through the use of such a procedure, the presence of the tumor associated antigen can be determined and/or the distribution of the antigen in the histological sample can be examined. Those of ordinary skill in the art will readily appreciate that any of a wide variety of histological methods (such as staining procedures) can be modified in order to achieve such in situ detection.

In some embodiments, a biological sample from a subject is contacted with and immobilized onto a matrix, such as, for example, nitrocellulose, or other solid support (see supra) which is capable of immobilizing cells, cell particles or polypeptides. The matrix can then be washed with suitable buffers followed by treatment with the labeled antibody. The matrix can then be washed with the buffer to remove unbound antibody. The amount of bound label on the matrix can be detected by conventional means.

Bound, labeled antibody can be detected by standard calorimetric, radioactive, photometric and/or fluorescent detection means. Detection reagents can be used, if needed. For fluorescent labels, signals can be detected by, for example, a scanning confocal microscope in photon counting mode. Appropriate scanning devices are described by, for example, U.S. Pat. Nos. 5,578,832 and 5,631,734 (both incorporated by reference herein). For antibodies labeled with biotin, the reaction can be treated with the appropriate streptavidin-conjugate (e.g., streptavidin-horseradish peroxidase, streptavidin-alkaline phosphatase, streptavidin-luciferase, and the like) and then treated with the appropriate reagents for calorimetric or photometric detection. For radiolabeled antibody, signals can be detected using a scintillation counter, phosphoimager or similar device.

In another aspect, diagnostic assays are provided to detect the expression of tumor associated antigen genes. Tumor associated antigen nucleic acid sequences, or fragments thereof comprising about at least 8 nucleotides, can be used as hybridization probes. Hybridization assays can be used to detect, prognose, diagnose, or monitor hyperproliferative disease associated with aberrant changes in tumor associated antigen expression and/or activity. In particular, such a hybridization assay can be carried out by a method comprising contacting a sample containing nucleic acids (target nucleic acids) with a nucleic acid probe capable of hybridizing to tumor associated antigen nucleic acid, under conditions such that hybridization can occur, and detecting or measuring any resulting hybridization.

In specific embodiments, hyperproliferative disease can be diagnosed, or its suspected presence can be screened for, or a predisposition to develop such disease can be detected, by detecting tumor associated antigen RNA associated with increased or altered expression of the tumor associated antigen. Suitable hybridization assays include, for example, Northern blots, dot blots, RT-PCR, quantitative PCR, and the like.

In a specific embodiment, levels of tumor associated antigen mRNA are detected or measured, in which increased levels indicate that the subject has, or has a predisposition to developing, a hyperproliferative disease. Diagnostic procedures can also be performed in situ directly upon, for example, tissue sections (e.g., fixed and/or frozen) of subject tissue obtained from biopsies or resections, such that no nucleic acid purification is necessary. Tumor associated antigen nucleic acids can be used as probes and/or primers for such in situ procedures (see, e.g., Nuovo, PCR In Situ Hybridization: Protocols and Applications, Raven Press, NY (1992), the disclosure of which is incorporated by reference herein).

Diagnostic methods for the detection of tumor associated antigen nucleic acids can also involve, for example, contacting and incubating nucleic acids from a subject sample with one or more labeled nucleic acids, under conditions favorable for the specific annealing of the nucleic acids to their complementary sequences. Typically, the lengths of these nucleic acid reagents are at least 15 to 30 nucleotides. After incubation, all non-annealed nucleic acids are removed. The presence of bound nucleic acids from the sample, if any such molecules exist, is then detected. Using such a detection scheme, the nucleic acid from the tissue or cell type of interest can be immobilized, for example, to a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads.

Nucleic acid arrays can be used to monitor the expression of tumor associated genes, such as, for example, Ubiquilin-1, IFI27, HOX-B6, ZFP161, YB-1, KIAA0136, Osteonectin, F-box only protein 21, and/or ILF3. Nucleic acid arrays can further be used to detect p53, and/or NY-ESO-1 gene expression. Typically, an array of polynucleotide probes is contacted with a sample of target nucleic acids to produce a hybridization pattern. The binding of the target nucleic acids to one or more probes of the array is then detected to obtain a qualitative and/or quantitative profile of expression of the tumor associated antigen gene.

An array of polynucleotide probes stably associated with the surface of a substantially planar solid support is typically contacted with a sample of target nucleic acids under hybridization conditions sufficient to produce a hybridization pattern of complementary probe/target complexes. A variety of different arrays can be used and are known in the art. The polymeric or probe molecules of the arrays can be polynucleotides or hybridizing derivatives or analogs thereof, including: nucleic acids in which the phosphodiester linkage has been replaced with a substitute linkage, such as phosphorothioate, methylimino, methyl-phosphonate, phosphoramidate, guanidine, and the like; nucleic acids in which the ribose subunit has been substituted, for example, hexose phosphodiester; peptide nucleic acids; and the like. The length of the probes will generally range from about 10 to about 1000 nucleotides. In some embodiments the probes will be oligonucleotides and usually range from about 15 to about 150 nucleotides and more usually from about 15 to about 100 nucleotides in length. In other embodiments the probes will be longer, usually ranging in length from about 150 to about 1000 nucleotides. The probes can be single or double stranded, usually single stranded, and can be PCR fragments amplified from cDNA. The probe molecules on the surface of the substrates will typically correspond to at least one of the tumor associated antigen genes and be positioned on the array at a known locations so that positive hybridization events can be correlated to expression of a particular gene in the physiological source from which the target nucleic acid sample is derived. Because of the manner in which the target nucleic acid sample is generated, as described below, the arrays of probes will generally have sequences that are complementary to the non-template strands of the gene to which they correspond.

The substrates with which the probe molecules are stably associated can be fabricated from a variety of materials, including plastics, ceramics, metals, gels, membranes, glasses, and the like. The arrays can be produced according to any convenient methodology, such as preforming the probes and then stably associating them with the surface of the support or growing the probes directly on the support. A number of different array configurations and methods for their production are known to those of skill in the art and disclosed in, for example, U.S. Pat. Nos.: 5,445,934; 5,532,128; 5,556,752; 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,561,071; 5,571,639; 5,593,839; 5,599,695; 5,624,711; 5,658,734; and 5,700,637; the disclosures of which are herein incorporated by reference.

The target nucleic acid is typically contacted with the array under conditions sufficient for hybridization of target nucleic acid to probe to occur. Suitable hybridization conditions are well known to those of skill in the art and reviewed in Sambrook et al. (supra) and PCT Patent Publication WO 95/21944 (incorporated by reference herein). For example, low stringency hybridization conditions can be at 50° C. and 6×SSC while hybridization under stringent conditions can be at 50° C. or higher and 0.1×SSC.

In one embodiment, the amount of tumor associated antigen nucleic acids in the sample can be quantitated. (See, e.g., U.S. Pat. No. 6,004,755, the disclosure of which is incorporated by reference herein.) For example, the target nucleic acids in the sample can be end-labeled in a manner such that each of the target nucleic acids in the sample produces a signal of the same specific activity. By generating the same specific activity is meant that each individual target polynucleotide in the sample being assayed is labeled in a manner such that the molecule is capable of providing the same signal (e.g., the same intensity of signal) as every other labeled target in the sample. Each of the target nucleic acids generates a signal of the same specific activity because the number of labeled nucleotide bases in each of the target molecules is either identical or substantially the same.

The label is capable of providing a detectable signal, either directly or through interaction with one or more additional members of a signal producing system. Labels that are directly detectable and that can find use in the subject invention include: fluorescent labels. The fluorescers of interest include fluorescers in which the wavelength of light absorbed by the fluorescer will generally range from about 300 to 900 nm, usually from about 400 to 800 nm. The absorbance maximum will typically occur at a wavelength ranging from about 500 to 800 nm. Specific fluorescers of interest for use in singly labeled primers include, for example, fluorescein, rhodamine, BODIPY, cyanine dyes and the like, and are further described in Smith et al (Nature 321:647-79 (1986)). Suitable radioactive isotopes include, for example, ³⁵S, ³²P, ³H, etc. Examples of labels that provide a detectable signal through interaction with one or more additional members of a signal producing system include capture moieties that specifically bind to complementary binding pair members, where the complementary binding pair members comprise a directly detectable label moiety, such as a fluorescent moiety as described above. Capture moieties of interest include ligands, such as, for example, biotin where the other member of the signal producing system could be fluorescently labeled streptavidin, and the like.

In some applications, it is desired to analyze populations of target nucleic acids from two or more samples. Such samples can be differentially labeled. Alternatively, targets nucleic acids from different samples are separately contacted to identical probe arrays under conditions of hybridization, typically stringent hybridization conditions, such that labeled nucleic acids hybridize to their complementary probes on the substrate surface, and the target nucleic acids bound to the array separately detected. A set of standard nucleic acid molecules can optionally be used. For example, the standard nucleic acids can be provided by reverse transcribing standard RNA.

Following hybridization, a washing step can be employed to remove non-specifically bound nucleic acid from the support surface, generating a pattern of hybridized nucleic acid on the substrate surface. A variety of wash solutions and protocols for their use are known to those of skill in the art and can be used.

Where the label on the target nucleic acid is not directly detectable, the array can be contacted with the other member(s) of the signal producing system that is being employed. For example, where the label on the target is biotin, the array can be contacted with streptavidin-fluorescer conjugate under conditions sufficient for binding between the specific binding member pairs to occur. Following contact, any unbound members of the signal producing system will then be removed (e.g., by washing). The specific wash conditions employed can depend on the specific nature of the signal producing system that is employed, and will be known to those of skill in the art familiar with the particular signal producing system employed.

The resultant hybridization pattern(s) of target nucleic acids bound to the array can be visualized or detected in a variety of ways, with the particular manner of detection being chosen based on the particular label of the nucleic acid. For example, detection means can include scintillation counting, autoradiography, fluorescence measurement, colorimetric measurement, light emission measurement, and the like.

Prior to detection or visualization, the array of hybridized target/probe complexes can be optionally treated with an endonuclease. The endonuclease degrades single stranded, but not double stranded DNA. A variety of different endonucleases are known and can be used. Such nucleases include, for example, mung bean nuclease, S1 nuclease, and the like.

Following detection or visualization, the hybridization pattern can be used to determine qualitative and/or quantitative information about the expression of tumor associated antigen genes. The hybridization patterns of different samples can be compared with each other, or with a control sample, to identify differences between the patterns. The hybridization arrays can also be used to identify differential gene expression, in the analysis of diseased and normal tissue (e.g., neoplastic and normal tissue), different tissue or subtissue types; and the like.

Kits for diagnostic use are also provided, that comprise in one or more containers a tumor associated antigen, and, optionally, anti-tumor associated antigen antibody. The tumor associated antigen can optionally be labeled (e.g., with a detectable marker, such as, for example, a chemiluminescent, enzymatic, fluorescent, and/or radioactive moiety). Kits for diagnostic use are also provided that comprise in one or more containers an anti-tumor associated antigen antibody, and, optionally, a labeled binding partner to the antibody. Alternatively, the anti-tumor associated antigen antibody can be labeled (with a detectable marker, such as, for example, a chemiluminescent, enzymatic, fluorescent, and/or radioactive moiety).

A kit is also provided that comprises in one or more containers a nucleic acid probe capable of hybridizing to tumor associated antigen RNA. In a specific embodiment, a kit can comprise in one or more containers a pair of primers (e.g., each in the size range of 6-30 nucleotides, or more in length) that are capable of priming amplification (e.g., by polymerase chain reaction (see, e.g., Innis et al., PCR Protocols, Academic Press, Inc., San Diego, Calif. (1990)), ligase chain reaction (see, e.g., EP 320,308), use of Qβ replicase, cyclic probe reaction, or other methods known in the art under appropriate reaction conditions, of at least a portion of a tumor associated antigen nucleic acid. A kit can optionally further comprise in a container a predetermined amount of at least one purified tumor associated antigen or nucleic acid, for example, for use as a standard or control.

The following examples are provided merely as illustrative of various aspects of the invention and shall not be construed to limit the invention in any way.

EXAMPLES Example 1

The following example describes the identification of tumor associated antigens using serum from patients having ovarian cancer.

SEREX Immunoscreening

RNA isolated from ten stage III/IV serous ovarian tumors was pooled and poly-A selected using an mRNA Separator kit from Clontech. Selected mRNA was converted to cDNA with a modified ZAP cDNA synthesis kit (Stratagene) and cloned into lambda TriplEx (Clontech). Prior to screening, serum from stage III ovarian cancer patients was pre-cleared of E. coli specific antibodies using an E. coli affinity resin (5Prime3Prime) according to the manufacturers instructions. SEREX immunoscreening was performed essentially as described by Tureci et al. (Hybridoma 18:23-28 (1999); Mol. Med. Today 3:342-49 (1997), both incorporated by reference herein). Briefly, aliquots of the expanded library were plated at 2×10³ PFU/100 mm plate, overlaid with IPTG impregnated nitrocellulose membranes and incubated overnight at 37° C. The following morning, lifts were washed three times in Tris buffered saline (TBS: 20 mM Tris-HCl pH 7.5 and 150 mM NaCl)+0.05% Tween 20, blocked in TBS+1% BSA for 2 hours and exposed to serum diluted 1:200 in TBS/BSA overnight at room temperature. Lifts were washed 3 times in TBS and incubated with an alkaline phosphatase-linked goat anti-human IgG secondary antibody for 45 minutes at room temp. After three washes in TBS, lifts were developed in nitro blue tetrazolium chloride/5-bromo-4-chloro-3-indoyl phosphate (NBT/BCIP) for approximately 5 minutes, stopped in water for 20 minutes and dried. Positive phage plaques were picked and stored in SM buffer (100 mM NaCl, 50 mM Tris-HCl pH 7.5 and 10 mM MgSO₄) at 4° C. with a drop of chloroform.

Antigen Validation

The primary clones were validated using a SEREX array protocol. Briefly, a small aliquot of each phage suspension was spotted onto a bacterial lawn in a defined position (an array). Multiple identical plates were constructed with identical phage arrays. Arrays were overlaid with IPTG impregnated nitrocellulose membranes and grown overnight as described for basic SEREX screening. Individual lifts were then exposed to serum from a single normal or cancer patient. In this manner, large numbers of normal and patient sera can be screened for antibodies to a large number of primary clones. Clones that bind serum antibodies present in one or more patient sera and not normal sera are classified as a tumor antigen.

Phage encoding tumor antigens were purified by SEREX screening plates infected with increasing dilutions of phage suspension. Isolated positive plaques were then picked and suspended in SM buffer, with a drop of chloroform. These purified phage were converted to plasmids by infecting Cre expressing hosts (BM25.8) according to the protocol provided with the lambda TriplEx vector (Clontech). Sequencing was carried out using ABI BigDye sequencing reagents.

Sequencing and Analysis

Sequencing templates were prepared using QIAprep mini spin columns according to the manufacturer's instructions. Both ends of clone all clones were sequenced using the following vector primers; TCCGAGATCTGGACGAGC (sense primer) (SED ID NO:1) and TAATACGACTCACTATAGGG (anti-sense primer) (SED ID NO:2). Sequences were analyzed using BLASTn searches against NCBI (http://www.ncbi.nlm.nih.gov/) nr, EST and Unigene databases.

Production of Tumor Associated Antigens for Sandwich ELISAs

Recombinant histidine-tagged versions of the tumor associated antigens are produced. The histidine tag (or “His tag”) contains 6 tandem histidine residues typically placed at the N- or C-terminus of the protein of interest. These 6 H is residues allow binding of protein to metal conjugated ELISA plates. If necessary, these proteins can be further purified prior to ELISA by metal chelate chromatography.

To produce His tagged versions of the tumor associated antigens, cDNA clones encoding the complete open reading frame of a tumor associated antigen are obtained or assembled. Once full-length cDNAs corresponding to the antigens of interest are sequenced, they are inserted into the mammalian expression vector pcDNA3.1/His (Invitrogen) or the bacterial expression vector pQE (Quiagen) and sequenced. These vectors fuse six histidine residues to the recombinant protein. The resulting pcDNA plasmids are transiently transfected into COS7 cells (a green monkey kidney cell line) using LIPOFECTAMINE™. The pQE constructs are transformed into the E. coli strain XL1-Blu using standard Calcium Phosphate transformation protocols. Expression of the recombinant antigens is assessed by Western blot of whole-cell lysates using an antibody to the His tag (Clontech); cells transfected with an empty His vector serve as a negative controls.

ELISA Protocol

Serum antibodies to tumor antigens are detected by ELISA. 96-well Ni-NTA H isSorb Plates ELISA plates (Quiagen) are incubated for 2 hours at 20° C. with an optimized solution of his-tagged antigen containing cellular lysate. After incubation, plates are washed with PBS/0.5% Tween-20 and then incubated with human serum samples diluted 1:25, 1:50, 1:100, and 1:200 (extended titration assays is performed for sera which does not titer at 1:200). All serum samples are diluted 1:50 in PBS/1% BSA/1% FBS (fetal bovine serum)/25 μg/ml mouse IgG/0.01% NaN₃ and then serially in PBS/1% BSA. Serum samples from cancer patients and normal controls are tested in duplicate. 50 μl of diluted serum is added per ELISA well for one hour at room temperature. After washing with PBS/1% BSA, goat anti-human antibody conjugated to horseradish peroxidase (HRP) is added to wells at a 1:5000 dilution in PBS/1% BSA and incubated for 45 min at room temperature and washed. Experiments are carried out using two different isotype specific secondary antibodies specific for human IgG and IgA. After washing plates with PBS/1% BSA, the developing reagent TMB (Kirkegaard and Perry Laboratories, Gaithersburg Md.) is added. The color reaction is monitored at 640 nm until the wells coated with 14 nanogram human Ig reach an optical density (OD) of 0.3, at which point the reaction is stopped by adding 1N HCl. Plates are read at 450 nm by an automated plate reader.

Example 2

The following Table 1 summarizes the results of the screening described in Example 1. Shown are the results for 31 ovarian cancer patients whose serum was tested for the presence of autoimmune antibodies to the antigens indicated in each column. All antigens tested negative against a panel of 20 sera from age-matched disease-free females. “XX” denotes sera that are clearly positive by SEREX methodology for autoimmune antibodies to a given antigen. “©” indicates screening serum, usually from a pool of two patients. “E++” indicates a positive result by ELISA. “ND” indicates the ELISA was not developed. Empty cells indicate no reactivity. TABLE 1 Patient Stage of Osteo- F-box Number Disease ESO Ubiquilin-1 IFI 27 P53 HOX-B6 ILF3 ZFP161 YB-1 KIAA0136 CD44 nectin prtn 1 IIIC © 2 IVA 3 IIIC XX XX © 4 IIIC XX © XX © E++ 5 IIIC 6 IIIC 7 IIIC XX © 8 IIIC XX XX E++ 9 IIIC 10 IVA © 11 I/II 12 I/II 13 IVA 14 I/II 15 IIIC 16 IIIC XX E++ 17 IVB XX E++ 18 IIIC © 19 IIIC 20 IIIC © 21 IIIC XX 22 I/II 23 IIIC XX © E++ 24 IVA © XX © © 25 IIIC XX XX © XX © E++ E++ © 26 IIIC XX © 27 IIIC © 28 I/II 29 IIIC © 30 IIIC XX XX E++ 31 XX © © Serex 5 4 2 2 1 1 1 1 1 1 1 1 ELISA ++ 4 2 ND 1 ND ND 1 ND ND ND ND ND TOTAL 5 4 2 2 1 1 1 1 1 1 1 1

The previous examples are provided to illustrate but not to limit the scope of the claimed inventions. Other variants of the inventions will be readily apparent to those of ordinary skill in the art and encompassed by the appended claims. All publications, patents, patent applications and other references cited herein are hereby incorporated by reference. 

1. A method for prognosis or diagnosis of autoimmune disease in a subject, comprising: obtaining a sample from the subject, the sample comprising antibodies; contacting the sample with at least one tumor associated antigen, the tumor associated antigen being ZFP161, Ubiquilin-1, HOX-B6, IFI27, YB-1, KIAA0136, Osteonectin, F-box only protein 21, or ILF3; and detecting complex formation between the tumor associated antigen and the antibodies in the sample; wherein complex formation indicates a prognosis or diagnosis of autoimmune disease.
 2. The method of claim 1, wherein the subject is a mammal.
 3. The method of claim 2, wherein the subject is human.
 4. The method of claim 1, wherein the sample is blood, serum, ascites fluid, mucosal fluid, cervical wash, nipple aspirate fluid, stool, urine, saliva, tears, or sputum.
 5. The method of claim 4, wherein the sample comprises serum.
 6. The method of claim 1, wherein the detecting is by Western blot, radioimmunoassay, ELISA, sandwich immunoassay, immunoprecipitation assay, precipitin reaction, gel diffusion precipitin reaction, immunodiffusion assay, agglutination assay, complement-fixation assay, immunoradiometric assay, fluorescent immunoassay or protein A immunoassay.
 7. The method of claim 1, wherein the at least one tumor associated antigen further comprises tumor suppressor p53 or cancer-testis antigen NY-ESO-1.
 8. The method of claim 1, wherein the autoimmune disease is rheumatoid arthritis, graft versus host disease, systemic lupus erythromatosis (SLE), scleroderma, multiple sclerosis, diabetes, organ rejection, inflammatory bowel disease, or psoriasis.
 9. The method of claim 1, further comprising: comparing the complex formation between the tumor associated antigen and the antibodies in the sample with complex formation of a standard to determine the prognosis or diagnosis of autoimmune disease. 